We just posted yet another pre-submission paper to arXiv.org:
Assembling large, complex environmental metagenomes
Authors: Adina Chuang Howe, Janet Jansson, Stephanie A. Malfatti, Susannah Tringe, James M. Tiedje, and C. Titus Brown
Abstract:
The large volumes of sequencing data required to deeply sample …read more
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We just posted another pre-submission paper to arXiv.org:
Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets
Authors: Adina Chuang Howe, Jason Pell, Rosangela Canino-Koning, Rachel Mackelprang, Susannah Tringe, Janet Jansson, James M. Tiedje, and C. Titus Brown
Abstract:
Sequencing errors and …read more
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This post can be referenced and cited at the following DOI: http://dx.doi.org/10.6084/m9.figshare.98198.
For a few months, the Trinity list was awash with discussions about how to use digital normalization to lower the memory and compute requirements for mRNASeq assembly. At some point …
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I recently had the pleasure of reviewing an excellent paper that used actual data (DATA!) to argue that source code needs to be part of the review process. (When it is published I will post again about it; for now, the process of secret handshakes in smoke-filled back rooms must …
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I am just returning from a trip to Southern California that included, among other things, the teaching of a two day Software Carpentry workshop at The Scripps Research Institute. There were two instructors, myself and Tracy Teal, a research scientist at MSU; and two external TAs, Qingpeng Zhang (one of …
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Just over a week ago, I posted a list of wanted tech that I thought would help further open science. One item that struck a chord with a number of people on Twitter and in the comments was the idea of giving blog entries a DOI:
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- An easy way to …
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I gave a talk last Wednesday at U. Michigan in the DCMB program where I included a slide estimating how much DNA sequencing (in base pairs) was needed for good de novo assembly of sequences from various biological environments or problems. The slide was there to motivate the challenges of …
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